Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CanS-JC.fastq.uq.polyn	CanS-JC.filter	percent
uq reads:	46995186	9150270	19.4707%
   reads: 	68674470	10695089	15.5736%
----------------
virus_structural_rna_repbase_filter:
  reads:	CanS-JC.filter	CanS-JC.nostrna	percent
uq reads:	9150270	9115211	99.6169%
   reads: 	10695089	10496495	98.1431%
----------------
TE_filter:
  reads:	CanS-JC.nostrna	CanS-JC.noTE	percent
uq reads:	9115211	9114011	99.9868%
   reads: 	10496495	10494822	99.9841%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-JC.noGEN.front	CanS-JC.noGEN.front.gen	percent
uq reads:	9114011	5942290	65.1995%
   reads: 	10494822	6317087	60.1924%
----------------
match_TE:2:
  reads:	CanS-JC.noGEN.front	CanS-JC.noGEN.front.TE	percent
uq reads:	9114011	705049	7.7359%
   reads: 	10494822	790706	7.5342%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-JC.noGEN.end	CanS-JC.noGEN.end.gen	percent
uq reads:	9114011	274232	3.0089%
   reads: 	10494822	428632	4.0842%
----------------
match_TE:2:
  reads:	CanS-JC.noGEN.end	CanS-JC.noGEN.end.TE	percent
uq reads:	9114011	51270	0.5625%
   reads: 	10494822	76503	0.7290%
----------------
Candidate insertion sites in file: CanS-JC_insert.txt
  reads:	18291
  uqreads:	12883
  Number of Candidate sites:	12883

Level 1 collapse of insertion sites in file: CanS-JC_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	625

Level 1 annotation file: CanS-JC_level1siteannotation.xls
Insertion sites in fixed bin:
CanS-JC_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CanS-JC.noGEN.front	CanS-JC.noGEN.front.gendel	percent
uq reads:	9114011	5942290	65.1995%
   reads: 	10494822	6317087	60.1924%
----------------
match_dm6_mask_gen_del:1:
  reads:	CanS-JC.noGEN.end	CanS-JC.noGEN.end.gendel	percent
uq reads:	9114011	274232	3.0089%
   reads: 	10494822	428632	4.0842%
----------------
Candidate breakpoint sites in file: CanS-JC_depletion.xls
  reads:	49520
  uqreads:	33497
  Number of reads supporting candidate sites:	33497

Level 1 collapse of depletion sites in file: CanS-JC_depletion_level1.xls
  Number of Level 1 collapsed sites:	2749